Thromboangiitis Obliterans (Buerger's Disease): This condition is characterized by inflammation and thrombosis of blood vessels, often affecting the limbs. The progression from lower to upper limbs and the involvement of multiple limbs could suggest this diagnosis, especially in a young male without other comorbidities.

Antiphospholipid Syndrome: Although the autoimmune workup was negative, antiphospholipid syndrome can sometimes present with atypical or low-titer antibodies. The syndrome is known for causing venous thrombosis, and its diagnosis might require more specific testing.
Hypercoagulable State: Conditions such as Factor V Leiden, protein C or S deficiency, or antithrombin III deficiency could lead to recurrent thrombophlebitis. Testing for these conditions might not have been included in the initial workup.
Infectious Causes (e.g., Lemierre's Syndrome): Despite the lack of response to initial antibiotics, a more unusual infectious cause could be considered, especially with the progression to the neck, which might suggest internal jugular vein thrombosis.

Disseminated Intravascular Coagulation (DIC): This condition, although rare, can cause widespread thrombosis and would be critical to identify due to its high mortality rate. It can be triggered by various factors, including severe infection or malignancy, despite initial negative workups.
Heparin-Induced Thrombocytopenia (HIT): If the patient was started on heparin for the initial thrombophlebitis, HIT is a potentially life-threatening condition that must be considered, especially if there's a drop in platelet count.

Malignancy-Associated Thrombophlebitis (Trousseau’s Syndrome): Although tumor markers and whole-body CT scans were negative, some malignancies can be occult or not detected by initial screening. This condition is rare but should be kept in mind, especially with the aggressive nature of the thrombophlebitis.
Behçet's Disease: A form of vasculitis that can cause thrombophlebitis among other symptoms. It's rare and might not have been initially suspected but could explain the multifocal nature of the thrombophlebitis.
Vasculitis (e.g., Giant Cell Arteritis, Polyarteritis Nodosa): Other forms of vasculitis could potentially cause these symptoms, although they might be less likely given the age and presentation of the patient.